The role of natural selection against the deleterious effects of individual transposable element insertions was investigated by comparing the numbers of transposable elements on the X chromosomes versus autosomes of Drosophila. There is little evidence for selection against copia-like elements on the X chromosomes. This suggests other possible mechanisms (e.g. chromosome rearrangement) are likely to be important in removing transposable elements from natural populations. A second study investigated the theory of the evolution of copy number regulation of a transposable element in an outbreeding population. The prediction of this study is that dominant effects, such as chromosome rearrangements, are likely to be the events that ultimately make the evolution of copy number regulation likely. Finally, the theory of the evolution of reduced recombination in centromeric and telomeric regions was developed and the associated accumulation of tandemly repeated DNA was investigated.